|
| Status |
Public on Dec 31, 2015 |
| Title |
CRTL 42 |
| Sample type |
RNA |
| |
|
| Source name |
plasma
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
age at interview: 45
smoking status: Ever smoker
disease state: Non-cancer
|
| Treatment protocol |
Peripheral blood was collected in EDTA tubes at the time of interview.
|
| Growth protocol |
n/a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 300L of plasma using NucleoSpin® miRNA Plasma kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s protocol with Proteinase K digest, addition of 2μg of glycogen carrier and DNAse digest steps. All samples were spiked-in with 10pmol of Arabidopsis thaliana synthetic miR-159a (synthesized by Eurofins MWG Operon, Ebersberg, Germany) to control for variations in the RNA preparation step.
|
| Label |
FAM
|
| Label protocol |
Expression levels of 754 miRNAs (Sanger miRBase v14) were quantified using the TaqMan Human MicroRNA Array A + B Card Set v3.0 (Applied Biosystems, Foster City, CA) as per the manufacturer's instructions (including pre-amplification).
|
| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
n/a
|
| Description |
Control
|
| Data processing |
The data were analysed in HTqPCR package using R Bioconductor. miRNAs with undetermined Ct values in more than 120 samples were filtered out. Data were quantile normalized. Following normalization Ct values with an interquartile range (IQR) of less than 1.5 and endogenous controls were removed from subsequent analysis, and limma analysis was performed to identify differentially regulated miRNA between cases and controls. With limma, a one-factorial linear model is fitted for each miRNA and the standard errors (SE) are moderated using an empirical Bayes model resulting in moderated t-statistics for each miRNA. These analysis were performed separately for CARD A and CARD B.
Matrix normalized worksheet reports normalized signal (quantile normalization). Fold Change worksheet reports fold changes across all cases and controls.
|
| |
|
| Submission date |
Dec 30, 2014 |
| Last update date |
Dec 31, 2015 |
| Contact name |
Magdalena B Wozniak |
| Organization name |
International Agency for Research on Cancer
|
| Department |
Genetic Epidemiology
|
| Street address |
150 cours Albert Thomas
|
| City |
Lyon |
| ZIP/Postal code |
69008 |
| Country |
France |
| |
|
| Platform ID |
GPL18942 |
| Series (1) |
| GSE64591 |
Circulating microRNAs as non-invasive biomarkers for early detection of non-small-cell lung cancer |
|
